Precise measurement of the self-diffusion coefficient for poly(ethylene glycol) in aqueous solution using uniform oligomers

Current advances in photocatalytic proximity labeling

Understanding the intricate network of biomolecular interactions that govern cellular processes is a fundamental pursuit in biology. Over the past decade, photocatalytic proximity labeling has emerged as one of the most powerful and versatile techniques for studying these interactions as well as uncovering subcellular trafficking patterns, drug mechanisms of action, and basic cellular physiology. In this article, we review the basic principles, methodologies, and applications of photocatalytic proximity labeling as well as examine its modern development into currently available platforms. We also discuss recent key studies that have successfully leveraged these technologies and importantly highlight current challenges faced by the field. Together, this review seeks to underscore the potential of photocatalysis in proximity labeling for enhancing our understanding of cell biology while also providing perspective on technological advances needed for future discovery.

Solvent-controlled formation of alkali and alkali-earth-secured cucurbituril/guest trimers

Cucurbit[7]uril (CB[7]) encapsulates adamantyl and trimethylsilyl substituents of positively charged guests in dimethyl sulfoxide (DMSO). Unlike in water or deuterium oxide, addition of a selection of alkali and alkali-earth cations with van der Waals radii between 1.0 and 1.4 Å (Na+, K+, Ca2+, Sr2+, Ba2+ and Eu3+) to the CB[7]/guest complexes triggers their cation-mediated trimerization, a process that is very slow on the nuclear magnetic resonance (NMR) time scale. Smaller (Li+, Mg2+) or larger cations (Rb+, Cs+ or NH4+) are inert. The trimers display extensive CH-O interactions between the equatorial and pseudo-equatorial hydrogens of CB[7] and the carbonyl rim of the neighboring CB[7] unit in the trimer, and a deeply nested cation between the three interacting carbonylated CB[7] rims; a counteranion is likely perched in the shallow cavity formed by the three outer walls of CB[7] in the trimer. Remarkably, a guest must occupy the cavity of CB[7] for trimerization to take place. Using a combination of semi-empirical and density functional theory techniques in conjunction with continuum solvation models, we showed that trimerization is favored in DMSO, and not in water, because the penalty for the partial desolvation of three of the six CB[7] portals upon aggregation into a trimer is less unfavorable in DMSO compared to water.

Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform

The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently "tag" proximal biomolecules. The physical distance that the probes diffuse determines the effective labeling radius of the PLP and is a critical parameter that influences the scale and resolution of interactome mapping. As such, by expanding the degrees of labeling resolution offered by PLPs, it is possible to better capture the various size scales of interactomes. At present, however, there is little quantitative understanding of the labeling radii of different PLPs. Here, we report the development of a superresolution microscopy-based assay for the direct quantification of PLP labeling radii. Using this assay, we provide direct extracellular measurements of the labeling radii of state-of-the-art antibody-targeted PLPs, including the peroxidase-based phenoxy radical platform (269 ± 41 nm) and the high-resolution iridium-catalyzed µMap technology (54 ± 12 nm). Last, we apply these insights to the development of a molecular diffusion-based approach to tuning PLP resolution and introduce a new aryl-azide-based µMap platform with an intermediate labeling radius (80 ± 28 nm).

Microfluidic Chip Device for In Situ Mixing and Fabrication of Hydrogel Microspheres via Michael-Type Addition

Hydrogel microspheres are sought for a variety of biomedical applications, including therapeutic and cellular delivery, sensors, and lubricants. Robust fabrication of hydrogel microspheres with uniform sizes and properties can be achieved using microfluidic systems that rely on droplet formation and subsequent gelation to form microspheres. Such systems work well when gelation is initiated after droplet formation but are not practical for timed gelation systems where gelation is initiated prior to droplet formation; premature gelation can lead to device blockage, variable microsphere diameter due to viscosity changes in the precursor solution, and limited numbers of microspheres produced in a single run. To enable microfluidic fabrication of microspheres from timed gelation hydrogel systems, an in situ mixing region is needed so that various hydrogel precursor components can be added separately. Here, we designed and evaluated three mixing devices for their effectiveness at mixing hydrogel precursor solutions prior to droplet formation and subsequent gelation. The serpentine geometry was found to be the most effective and was further improved with the inclusion of a pillar array to increase agitation. The optimized device was shown to fully mix precursor solutions and enable the fabrication of monodisperse polyethylene glycol microspheres, offering great potential for use with timed gelation hydrogel systems.

Design and recognition of cucurbituril-secured platinum-bound oligopeptides

Platinum terpyridyl complexes, stacked on top of one another and secured as dimers with cucurbit[8]uril (CB[8]) in aqueous medium, were functionalized quantitatively and in situ with a pair of pentapeptides Phe-(Gly)₃-Cys by grafting their cysteine residues to the Pt centers. The resulting CB[8]·(Pt·peptide)₂ assemblies were used to target secondary hosts CB[7] and CB[8] via their pair of phenylalanine residues, again in situ. A series of well-defined architectures, including a supramolecular “pendant necklace” with hybrid head-to-head and head-to-tail arrangements inside CB[8], were obtained during the self-sorting process after combining only 3 or 4 simple building units.

A platinum terpyridyl complex, pentapeptide Phe-(Gly)₃-Cys and cucurbit[8]uril assemble into a “pendant necklace” with hybrid head-to-head and head-to-tail arrangements in aqueous medium.

Permeation of polyethylene glycols across the tympanic membrane

Localized and non-invasive delivery of therapeutics across barriers in the body is challenging. Examples include the flux of drugs across the tympanic membrane (TM) for the treatment of middle ear infections, and across the round window to treat inner ear disease. With the emergence of macromolecular therapies, the question arises as to whether such delivery can be achieved with macromolecules. Here, we have used polyethylene glycols (PEGs) in solutions to investigate macromolecular permeation across the TM in the chinchilla ex vivo. As the molecular weight of PEG increased, flux across the TM decreased, with an exponential relationship between the apparent diffusion coefficient and the molecular weight of the polymers. PEG flux was further decreased if it was released from a poloxamer 407 hydrogel, and lessened with increasing hydrogel concentration. Our results provide a framework for understanding the permeation of macromolecules noninvasively across barriers.

Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions

Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.

Solvation of nonionic poly(ethylene oxide) surfactant Brij 35 in organic and aqueous-organic solvents

HYPOTHESIS

By combining the experimental small- and wide-angle x-ray scattering (SWAXS) method with molecular dynamics simulations and the theoretical 'complemented-system approach' it is possible to obtain detailed information about the intra- and inter-molecular structure and dynamics of the solvation and hydration of the surfactant in organic and mixed solvents, e.g., of the nonionic surfactant Brij 35 (C₁₂E₂₃) in alcohols and aqueous alcohol-rich ternary systems. This first application of the complemented-system approach to the surfactant system will promote the use of this powerful methodology that is based on experimental and calculated SWAXS data in studies of colloidal systems. By applying high-performance computing systems, such an approach is readily available for studies in the colloidal domain.

EXPERIMENTS

SWAXS experiments and MD simulations were performed for binary Brij 35/alcohol and ternary Brij 35/water/alcohol systems with ethanol, n-butanol and n-hexanol as the organic solvent component at 25 °C.

FINDINGS

We confirmed the presence of solvated Brij 35 monomers in the studied organic media, revealed their preferential hydration and discussed their structural and dynamic features at the intra- and inter-molecular levels. Anisotropic effective surfactant molecular conformations were found. The influence of the hydrophobicity of the organic solvent on the hydration phenomena of surfactant molecules was explained.

Inferring the role of pit membranes in solute transport from solute exclusion studies in living conifer stems

The functional role of pits between living and dead cells has been inferred from anatomical studies but amassing physiological evidence has been challenging. Centrifugation methods were used to strip water from xylem conduits, permitting a more quantitative gravimetric determination of the water and solid contents of cell walls than is possible by more traditional methods. Quantitative anatomical evidence was used to evaluate the water volume in xylem conduits and the water content of living cells. Quantitative perfusion of stems with polyethylene glycol of different molecular weight was used to determine the solute-free space. We measured the portioning of water and solute-free space among anatomical components in stems and demonstrated that lignin impeded the free movement of solutes with molecular weight >300. Hence, movement of large solutes from living cells to xylem conduits is necessarily confined to pit structures that permit transmembrane solute transport via primary walls without lignin. The functional role of pits was additionally indicated by combining data in this paper with previous studies of unusual osmotic relationships in woody species that lack pits between dead wood fibers and vessels. The absence of pits, combined with the evidence of exclusion of solutes of molecular weight >300, explains the unexpected osmotic properties.

Sequence-Specific Self-Assembly of Positive and Negative Monomers with Cucurbit[8]uril Linkers

The self-assembly into dynamic oligomers of Cucurbit[8]uril (CB[8]), a positive ditopic Ir(III) bis-terpyridine complex, and a negative ditopic Fe(II) bis-terpyridine complex flanked by four butyrate side chains was assessed to answer a seemingly straightforward question: does CB[8] adopt a social self-sorting pattern by encapsulating both positive and negative units into a heteroternary complex? We showed that this is indeed the case, with CB[8] linking a positive Ir unit to a neighboring negative Fe unit whenever possible. Furthermore, the solubility of the dynamic oligomers was significantly affected by their sequence; upon addition of 0.6-1.2 equiv of positive Ir oligomer to its negative Fe counterpart, the predominant assembly present in solution was a mixed oligomer with a (Fe-Ir-Ir-) _n sequence. Weak interactions between the negative butyrate side chains and the partially positive outer wall of CB[7] were also identified by two-dimensional nuclear magnetic resonance techniques, and resulted in a negative p K_a shift (0.10 p K_a unit) for the terminal carboxylic groups.

Bactericidal Hydrogels via Surface Functionalization with Cecropin A

The immobilization of antimicrobial peptides (AMPs) to surfaces, enabling their utilization in biosensor and antibacterial/antifouling coating applications, is typically performed using rigid, solid support materials such as glass or gold and may require lengthy, temperamental protocols. Here, we employ a hydrogel immobilization platform to afford facile fabrication and surface functionalization while offering improved biocompatibility for evaluating the influence of linker length, surface density, and AMP conjugation site on retained peptide activity. Rapid, interfacial photo-polymerization using the radical-mediated thiol-ene addition mechanism was used to generate cross-linked, polymeric coatings bearing residual thiol moieties on prefabricated poly(ethylene glycol) (PEG)-based hydrogel supports. The photo-polymerized coatings were 60 μm thick and contained 0.55 nmol of unreacted free thiols, corresponding to a concentration of 410 μM, for use as cecropin A (CPA) immobilization handles via thiol-maleimide conjugation, where the CPA-bound maleimide moiety was localized at either the carboxyl terminus or midsequence between Ala₂₂ and Gly₂₃. Surface presentation of the thiol handles was controlled by varying the thiolated PEG monomer (PEGSH) used in the photo-polymerizable formulation. Bactericidal activity of CPA functionalized hydrogels against E. coli K235 indicated that CPA immobilized at the carboxyl terminus killed 94 ± 6% of the inoculated pathogens when coatings were prepared with high molecular weight PEGSH and 99 ± 1% when prepared with low molecular weight PEGSH. E. coli cell death demonstrated a stronger dependence on peptide concentration than PEG linker length or degree of thiol functionalization, with activity ranging from 34 ± 13% to 99 ± 1% bacterial cells killed as the prefunctionalization thiol concentration in the coatings was increased from 90 to 990 μM. Finally, the immobilization site on the surface-bound CPA strongly affected antibacterial activity; when midsequence modified CPA was bound to a hydrogel coating bearing 990 μM thiol, only 20 ± 4% of the E. coli population was killed.

Genetically targeted fluorogenic macromolecules for subcellular imaging and cellular perturbation

The alteration of cellular functions by anchoring macromolecules to specified organelles may reveal a new area of therapeutic potential and clinical treatment. In this work, a unique phenotype was evoked by influencing cellular behavior through the modification of subcellular structures with genetically targetable macromolecules. These fluorogen-functionalized polymers, prepared via controlled radical polymerization, were capable of exclusively decorating actin, cytoplasmic, or nuclear compartments of living cells expressing localized fluorgen-activating proteins. The macromolecular fluorogens were optimized by establishing critical polymer architecture-biophysical property relationships which impacted binding rates, binding affinities, and the level of internalization. Specific labeling of subcellular structures was realized at nanomolar concentrations of polymer, in the absence of membrane permeabilization or transduction domains, and fluorogen-modified polymers were found to bind to protein intact after delivery to the cytosol. Cellular motility was found to be dependent on binding of macromolecular fluorogens to actin structures causing rapid cellular ruffling without migration.

Stabilization of cucurbituril/guest assemblies via long-range Coulombic and CH···O interactions

Cucurbit[n]urils (CB[n], n = 6-8) interact strongly with metal-bound 4'-substituted terpyridine ligands (M = Fe(II) and Ir(III)) via CH···O hydrogen bonding, despite significant separation between the positive metallic cation and the carbonylated rim of CB[n], and the location of the latter in the second coordination sphere of the metal ion. While water has been shown to mediate interactions between cations and CB[n]s in some assemblies, mediation by organic ligands is unprecedented. The recognition process is driven by the contrasted combination of extremely favorable binding enthalpies (up to 20.2 kcal/mol) and very unfavorable entropic components (as low as -10.2 kcal/mol). Dynamic oligomers were prepared in the presence of CB[8], which acts as a "soft", noncovalent linker between metal/terpyridine complexes, and interconnects two 4'-substituents inside its cavity. Social self-sorting between CB[8] and metal/terpyridine complexes bearing 4'-(2-naphthyl) and 4'-(2,3,5,6-tetrafluorophenyl) substituents was also observed, and could afford well-organized oligomers with alternating Fe(II) and Ir(III) cations.

Coarse-grained simulations of rapid assembly kinetics for polystyrene-b-poly(ethylene oxide) copolymers in aqueous solutions

We present a coarse-grained, implicit solvent model for polystyrene-b-poly(ethylene oxide) in aqueous solution and study its assembly kinetics using Brownian dynamics simulations. The polymer is modeled as a chain of freely jointed beads interacting through effective potentials. Coarse-grained force field parameters are determined by matching experimental thermodynamic quantities including radius of gyration, second virial coefficient, aggregation number, and critical micelle concentration. We investigate the influence of cooling rate (analogous to the rate of solvent quality change in rapid precipitations), polymer concentration, and friction coefficient on the assembly kinetics and compare simulation results to flash nanoprecipitation experiments. We find that assembly kinetics show a linear scaling relation with inverse friction coefficient when the friction coefficient is larger than 1. When the cooling time is less than the characteristic micellization time, stable kinetically arrested clusters are obtained; otherwise, close-to-equilibrium micelles are formed. The characteristic micellization time is estimated to be only 3-6 ms, in contrast to 30-40 ms previously determined in experiments. We suggest that previous experiments probed the formation of micellar clusters while simulations in this work studied the kinetics of a single micelle assembled from free polymer chains.